Help Privacy Policy Disclaimer
  Advanced SearchBrowse





Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT


Kocher,  Arthur
Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute of Geoanthropology, Max Planck Society;

External Resource


Source Data
(Supplementary material)

Underlying Data
(Supplementary material)

Fulltext (restricted access)
There are currently no full texts shared for your IP range.
Fulltext (public)

(Preprint), 4MB

Supplementary Material (public)
There is no public supplementary material available

Borry, M., Forsythe, A., Valtueña, A. A., Hübner, A., Ibrahim, A., Quagliariello, A., et al. (2023). Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. F1000Research, 12: 926. doi:10.12688/f1000research.134798.1.

Cite as: https://hdl.handle.net/21.11116/0000-000D-8BC9-4
Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.github.io) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.

Methods: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate automated metadata curation and data validation, as well as rapid data filtering and downloading.

Results: AncientMetagenomeDir was extended to include standardised metadata of over 5000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.

Conclusions: Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.